Also, regarding your services not being visible in the REST services directory, I am wondering if you recently upgraded from 10.1 to 10.2.2. Were the services visible in 10.2.2 before or is this the first time you've gone to look at the services directory since the upgrade? I only ask because I've seen similar issues as you're describing after upgrades have been made but those particular ArcGIS for Server sites had not been re-authorized with a 10.2.2 ECP.